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19 results for “reaction energy”
Dataset for "Methodology of Evaluating the Activation Energy of Oxygen Reduction Reaction on Pt-based Electrodes"
<p>High temperature proton-exchange membrane fuel cell (HT-PEMFC) technology is widely studied alternative to current energy conversion technologies based on fossil fuels. Compared to solid oxide fuel cells (SOFCs), HT-PEMFCs allow more flexibility and demand less operation control due to their lower temperature. On the other hand, HT-PEMFCs show an advantage over low-temperature PEMFCs in terms of less demand on the purity of the H2 used, the possibility to recover the generated heat, lower water management requirements, and easy heat management. One of the critical limitations of HT-PEMFC operation is a slow kinetics of the cathodic reduction of O2 (ORR) due to presence of H3PO4 which ensures proton conductivity in the system. Electrochemical dynamic methods such as cyclic voltammetry or linear sweep voltammetry (LSV) can be used to determine the kinetic parameters of ORR. These measurements can provide information on the Tafel slope and exchange current density (jex) of the ORR. However, performing these measurements under conditions relevant for HT-PEMFC operation is challenging due to presence highly concentrated H3PO4 and elevated temperature. First, determination of the kinetic parameters requires correct assessment of equilibrium potential of ORR (EORR). The value of the EORR is generally influenced by the activity (fugacity) of the reactants and products and the temperature, a discussion of the appropriate standard states of the components is also necessary. Second, the relationship between the jex and the reaction rate constant (k°), necessary for calculation of activation energy ( ), must be known. It includes consideration of the likely reaction mechanism. In this paper, the methodology for appropriate determination of was developed and used for estimation of of ORR from LSV curves measured on commercially available Pt/C catalyst under HT-PEMFC relevant conditions. In particular, the measurements were carried out using a rotating glassy carbon rod disk electrode (RRE) in purified 98 wt.% H3PO4 (as electrolyte) at temperatures of 120, 140, 160, 180 °C. Though the treatment was developed in context of ORR and HT-PEMFC, the approach is generally applicable to any electrochemical reaction.</p>
Optimized structures of the stationary points on the potential energy surface of the OH(2Π) + C2H4 reaction
<p>This Zip file contains the cartesian coordinates of optimized stationary points of the OH(<sup>2</sup>Π) + C<sub>2</sub>H<sub>4</sub> potential energy surface published in our article “OH(<sup>2</sup>Π) + C<sub>2</sub>H<sub>4</sub> Reaction: A Combined Crossed Molecular Beam and Theoretical Study” (P<em>hys. Chem. A</em> 2023, 127, 21, 4609–4623), that can be found in <a href="https://doi.org/10.1021/acs.jpca.2c08662">https://doi.org/10.1021/acs.jpca.2c08662</a>.</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.</p>
Optimized structures of the stationary points on the potential energy surface of the O(3P, 1D) + HCCCN(X1Σ+) reaction
<p>This Zip file contains the cartesian coordinates of optimized stationary points of the O(<sup>3</sup>P, <sup>1</sup>D) + HCCCN(X<sup>1</sup>Σ<sup>+</sup>) potential energy surface published in our article “Reactions O(<sup>3</sup>P, <sup>1</sup>D) + HCCCN(X<sup>1</sup>Σ<sup>+</sup>) (Cyanoacetylene): Crossed-Beam and Theoretical Studies and Implications for the Chemistry of Extraterrestrial Environments” (<em>J. Phys. Chem. A</em> 2023, 127, 3, 685–703), that can be found in <a href="https://doi.org/10.1021/acs.jpca.2c07708">https://doi.org/10.1021/acs.jpca.2c07708</a>.</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.</p>
Dataset supporting the paper "Power discontinuity and shift of the energy onset of a molecular de-bromination reaction induced by hot-electron tunneling. Nanoscale 13, 15215 (2021)"
<p>Dataset corresponding to theoretical calculations in the paper "Power discontinuity and shift of the energy onset of a molecular de-bromination reaction induced by hot-electron tunneling. Nanoscale 13, 15215 (2021)". DOI: <a href="https://doi.org/10.1039/D1NR04229G">10.1039/D1NR04229G</a></p> <p>List of files:</p> <p>Several folders corresponding to the figures of the paper. They contain:</p> <ul> <li>CONTCAR files: relaxed structures in VASP format. They can be visualized with VESTA (<a href="https://jp-minerals.org/vesta/en/">https://jp-minerals.org/vesta/en/</a>).</li> <li>.agr: grace files (<a href="https://plasma-gate.weizmann.ac.il/Grace/">https://plasma-gate.weizmann.ac.il/Grace/</a>).<br> </li> </ul>
Data deposit accompanying Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields
<p>Dataset accompanying the paper: <em>"Accurate Energy Barriers for Catalytic Reaction Pathways: An Automatic Training Protocol for Machine Learning Force Fields"</em>. Contains the training sets curated during active learning as well as .xyz files used for creating the Figures. <br> <br> The paper highlights that the computational efficiency of ML force fields not only results in decreased computational costs for routine catalytic investigations but also facilitates more comprehensive exploration of catalytic pathways.</p> <p><strong>Published in NPJ Computational Materials</strong>: <a href="https://www.nature.com/articles/s41524-023-01124-2">https://www.nature.com/articles/s41524-023-01124-2</a><br> Formerly on Arxiv: <a href="https://arxiv.org/abs/2301.09931">https://arxiv.org/abs/2301.09931</a></p>
Optimized stationary points on the potential energy surface of the reaction of atomic oxygen O(3P) with acrylonitrile
<p>This Zip file contains the cartesian coordinates of optimized stationary points of the O(<sup>3</sup>P) + acrylonitrile potential energy surface (PES).</p> <p>The PES has been published in our article “A Computational Analysis of the Reaction of Atomic Oxygen O(<sup>3</sup>P) with Acrylonitrile”</p> <p>(<em>Lecture Notes in Computer Science</em> <strong>2021</strong>, 12958, 339-350), that can be found in https://doi.org/10.1007/978-3-030-87016-4_25 .</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.</p>
Optimized stationary points on the potential energy surfaces of the N(2D) + CH2CHCN and CN + CH2CHCN reactions
<p>This Zip file contains the cartesian coordinates of optimized stationary points on the potential energy surfaces (PESs) of two reactions: N(<sup>2</sup>D) + CH<sub>2</sub>CHCN (acrylonitrile) and CN + CH<sub>2</sub>CHCN.</p> <p>The PES has been published in our article “A Theoretical Investigation of the Reactions of N(<sup>2</sup>D) and CN with Acrylonitrile and Implications for the Prebiotic Chemistry of Titan”</p> <p>(<em>Lecture Notes in Computer Science</em> <strong>2022</strong>, 13378, 246-259), that can be found in https://doi.org/10.1007/978-3-031-10562-3_18 .</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.</p>
Optimized stationary points on the potential energy surfaces of the N(2D)+ C2H4 and N(2D)+ CH2CHCN reactions
<p>This Zip file contains the cartesian coordinates of optimized stationary points on the potential energy surfaces (PESs) of two reactions: N(<sup>2</sup>D)+ C<sub>2</sub>H<sub>4</sub> and N(<sup>2</sup>D)+ CH<sub>2</sub>CHCN.</p> <p>The PESs have been published in our article “Computational Investigation of the N(<sup>2</sup>D)+ C<sub>2</sub>H<sub>4</sub> and N(<sup>2</sup>D)+ CH<sub>2</sub>CHCN Reactions: Benchmark Analysis and Implications for Titan’s Atmosphere”</p> <p>(<em>Lecture Notes in Computer Science</em> <strong>2023</strong>, 14105, 705-717), that can be found in https://doi.org/10.1007/978-3-031-37108-0_45 .</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pVTZ level of theory.</p>
Optimized stationary points on the potential energy surfaces of the S+(4S) + SiH2(1A1) and HSiS+/SiSH+ + NH3 reactions
<p>This Zip file contains the cartesian coordinates of optimized stationary points on the potential energy surfaces (PESs) of three reactions: S<sup>+</sup>(<sup>4</sup>S) + SiH<sub>2</sub>(<sup>1</sup>A<sub>1</sub>), <sup>3</sup>HSiS<sup>+</sup> + NH<sub>3</sub> and <sup>3</sup>SiSH<sup>+</sup> + NH<sub>3</sub>.</p> <p>These PESs are part of our paper “The S<sup>+</sup>(<sup>4</sup>S)+SiH<sub>2</sub>(<sup>1</sup>A<sub>1</sub>) Reaction: Toward the Synthesis of Interstellar SiS”</p> <p>(<em>Lecture Notes in Computer Science</em> <strong>2022</strong>, 13378, 233-245), that can be downloaded in https://doi.org/10.1007/978-3-031-10562-3_17 .</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at B3LYP/aug-cc-pV(T+d)Z level of theory.</p>
Optimized structures of selected stationary points on the potential energy surface of the HC3N + CN reaction
<p>This Zip file contains the cartesian coordinates of optimized stationary points of the HC<sub>3</sub>N + CN potential energy surface published in our article “Semiempirical Potential in Kinetics Calculations on the HC<sub>3</sub>N + CN Reaction” (<em>Molecules</em> <strong>2022</strong>, <em>27(7)</em>, 2297), that can be found in <a href="https://doi.org/10.3390/molecules27072297">https://doi.org/10.3390/molecules27072297</a> .</p> <p>All calculations have been performed with Gaussian 09, Revision D.01.</p> <p>All structures have been optimized at M06-2X/6-311+G(d,p) level of theory.</p>
Dataset: 800 QM/MM minimum energy pathway conformations for the acylation reactions of Toho-1/ampicillin and Toho-1/cefalexin
<p>This dataset consists of 800 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the acylation reactions between a Class A beta-lactamases (Toho-1) and two beta-lactam antibiotic molecules (ampicillin and cefalexin).</p> <p>These files are:</p> <ul> <li>toho_amp.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_amp.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Ampicillin (200 pathways);</li> <li>toho_cex.r1-ae.zip: The R1-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>toho_cex.r2-ae.zip: The R2-AE acylation pathways for Toho-1/Cefalexin (200 pathways);</li> <li>energies.zip: the replica energies at B3LYP-D3/6-31+G**/C36 level;</li> <li>chelpgs.zip: the ChElPG charges of all reactant replicas at B3LYP-D3/6-31+G**/C36 level;</li> <li>farrys.zip: the featurzied NumPy arrays for model training;</li> <li>peephole.zip: an example file for how the optimized MEPs look like; </li> <li>dftb3_benchmark.zip: the reference calculations to justify the use of DFTB3/3OB-F/C36 in MEP optimizations, the reference level of theory is B3LYP-D3/6-31G**/C36. </li> </ul> <p>The R1-AE pathways are the acylation uses Glu166 as the general base; the R2-AE pathways uses Lys73 and Glu166 as the concerted base. </p> <p>All QM/MM pathways are optimized at the DFTB3/3OB-f/CHARMM36 level of theory. </p> <p>Z. Song et al Mechanistic Insights into Enzyme Catalysis from Explaining Machine-Learned Quantum Mechanical and Molecular Mechanical Minimum Energy Pathways. <em>ACS Phys. Chem Au</em> 2022, <strong>2</strong>, 4, 316–330. DOI: <a href="https://doi.org/10.1021/acsphyschemau.2c00005">10.1021/acsphyschemau.2c00005</a></p>
Thermodynamic database and calculator of free energies and potentials for redox reactions involving iron minerals in aqueous media (IMTD)
<p>Database of free energies of formation for iron minerals and associated aqueous species, which are used in a tableu style spreadsheet to calculate free energies of redox reactions involving iron minerals, which in turn are used to calculate free energies and formal potentials for these reactions, under specified environmental conditions.</p> <p>The database and calculators were assembled by students and postdocs (Jeff Hudson, Ania Pavitt, Ying Lan, and Miranda Bradley) working under direction of Professor Paul G. Tratnyek at the Oregon Health & Science University, Portland, Oregon, USA. Drew Latta, Thomas Robinson, and Michelle Scherer contributed to the database and extended the calculations.</p> <p>Early versions of this tool were used in several publications, including (i) Fan, D., Y. Lan, P. G. Tratnyek, R. L. Johnson, J. Filip, D. M. O'Carroll, A. N. Garcia, and A. Agrawal. 2017. <em>Environ. Sci. Technol.</em> 51(22): 13070–13085. [DOI: 10.1021/acs.est.7b04177] and (ii) Bradley, M. J., and P. G. Tratnyek. 2019. <em>ACS Earth & Space Chemistry</em> 3(3): 688-699. [DOI: 10.1021/acsearthspacechem.8b00200].</p> <p>This tool is provided as a spreadsheet in .xlsx format. The file includes six sheets. The first contains background, constants, and calculations that apply throughout the remaining tabs. The second contains free energies of formation from various authoritative sources, and a mechanism for designating “recommend values”. The third contains a tableu that calculates free energies of redox reactions using the recommended free energy of formation and user-specified stoichiometries. The fourth calculates free energies and formal potentials of the redox reactions using the standard potentials, and specific solution conditions. The last tab summarizes previous published formal potentials from a variety of sources. </p> <p>While the database was checked thoroughly, it still is unlikely to be completely accurate. For critical applications, we recommend that you track-down the primary sources (listed on the first tab of the spreadsheet) and use them for data, conditions, and other caveats. Obviously, we do not accept any responsibility for what anyone does with information obtained from this document.</p> <p>In the future, if significantly corrections or additions are made to this document, we may publish it here as new versions. If the contributions of others result in major improvements, we are open to adding new authors to those versions. Feel free to contact us with corrections, suggests, or offers to help.</p> <p>The development of this version of the tool was funded through grants from the Strategic Environmental Research and Development Program (SERDP) and the U.S. Department of Energy.</p>
Why The Perfectly Symmetric Cobalt-Pentapyridyl Loses the H2 Production Challenge: Theoretical Insight into Reaction Mechanism and Reduction Free Energies
<p>Abstract</p> <p>Researchers have extensively investigated photo-catalytic water reduction utilizing Cobalt-based catalysts with poly-pyridyl ligands. While catalysts exhibiting distorted poly-pyridyl ligand demonstrate higher H2 production yields, those with ideal octahedral coordination display poor performance. This outcome suggests the crucial role of ligand framework in catalytic activity, yet reasons behind the disparity in H2 production rates for catalysts with octahedral geometries remain unclear. We theoretically examined the water reduction mechanism of Co-based poly-pyridyl catalyst, CoPy5, having perfect octahedral coordination. We clarified the effect of octahedral coordination by utilizing each intermediate step of ECEC mechanism. We determined spin states, solvent response, electronic structures, and reduction free energies. CoPy5 with perfect octahedral coordination, alongside its distorted counterparts, exhibit similar spin states as the reaction progresses through each intermediate step. However, the first reduction free energy obtained for the CoPy5 is slightly higher than that of its distorted counterparts. Following the second protonation, resulting H2 molecule experiences limited diffusion from the Co center due to the compact structure of the CoPy5, which blocks the Co center for the next H2 production cycle. Catalysts having distorted octahedral geometries facilitate fast removal of H2 into the solvent. Thus, the reaction center becomes immediately available for subsequent H2 production.</p> <p>Computational Details</p> <p>AIMD simulations have been performed for modeling intermediate states of the ECEC mechanisms of H2 production through water splitting. Open source CP2K simulation package have been used in all simulations. PBE density functional in general gradient approximation (GGA) formalism was employed for the AIMD simulations. Goedecker-Teter-Hutter (GTH) potentials were applied for the estimation of core electron interactions with the valence shell and nucleus. Valence electrons were modeled explicitly and valence shells of Co, N, C, O and H contain 17, 5, 4, 6 and 1 electrons, respectively. DZVP-MOLOPT basis set was used for all atomic kinds. For auxiliary plane wave basis set, a cutoff of 400 Ry was utilized. Dispersion interactions were taken into consideration by applying Vydrov and Van Voorhis vdW density functional, in the revised form (rVV10). Periodic boundary<br> conditions and spin polarization were always applied. For the CoPy5 complex, AIMD simulations were carried out in a box defined as cubic with explicit water environment. The CoPy5 catalyst was first solvated in 215 water molecules and the simulation volume was relaxed by performing AIMD simulations for approximately 20 ps in the isothermal-isobaric ensemble (NPT). Cubic simulation box volume was determined as 6163.28 ̊A3. Following the determination of the simulation box size, each intermediate step were modeled by applying AIMD simulations in the canonical ensemble (NVT) for approximately 20 ps. Time step was set to 0.5 fs. Canonical sampling through velocity rescaling (CSVR) thermostat with a time constant of 100 fs was applied in order to keep<br> the simulation temperature at 300 K.</p> <p>Please see the corresponding article for more details.</p>
Dataset: 1,000 QM/MM minimum energy pathway conformations for the deacylation reactions of GES-5/imipenem
<p>This dataset consists of 1,000 coordinate files (in the CHARMM psf/cor format) for the QM/MM minimum energy pathways of the deacylation reactions between a Class A beta-lactamases (GES-5) and the imipenem antibiotic molecules.</p> <p>All pathway conformations were optimized at DFTB3/3OB-f/CHARMM36 level with 36 replicas.</p> <p>All single point calculations and charge population analysis were done at B3LYP-D3/6-31+G(d,p)/CHARMM36 level.</p> <ul> <li>0.paths_ges_imi_d1.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>0.paths_ges_imi_d2.tar.gz: 500 pathway conformations for GES-5/IPM-Delta1 deacylation reactions.</li> <li>1.eners.zip: The single point replica energies along all GES-5/IPM pathways.</li> <li>1.chrgs.zip: The NBO charges of the QM region of all replica conformations along all GES-5/IPM pathways.</li> <li>2.datasets.zip: The Python codes to postprocess the molecular data and the featurized the NumPy arrays.</li> <li>3.gnn.zip: The Python codes that implements the edge-conditioned graph convolutional NN to predict the deacylation barriers.</li> <li>5.representative_conf.zip: The pathway conformations of all cluster centroids and an energetic representative (pathway id 22) pathway. Note: This file also serves as a peephole of how the pathway conformations from Reaction Path with Holonomic Constrains calculations looks like.</li> <li>6.benchmark.zip: The benchmark calculations that validates the DFTB3/3OB-f/CHARMM36 against DFTB3/3OB/CHARMM36 and B3LYP/6-31G(d,p)/CHARMM36 level of theory on the energetic representative (pathway id 22) pathway conformations. </li> <li>p.figures.zip: A series of Jupyter Notebooks that produces the visualizations in the work.</li> <li>README.md: A markdown file that contains additional descriptions.</li> <li>environment.yml: The Conda environment used for the graph-learning. </li> </ul> <p>Z. Song and P. Tao, Graph-Learning Guided Mechanistic Insights into Imipenem Hydrolysis in GES Carbapenemases. <strong><em>Electron. Struct.</em></strong> 2022, <strong>4</strong>, 034001. DOI: <a href="https://doi.org/10.1088/2516-1075/ac7993">10.1088/2516-1075/ac7993</a></p>
DATASET for Biomethanol production via electrolysis, oxy-fuel combustion, water-gas shift reaction, and LNG cold energy recovery
<p>DATASET for the paper entitled: Biomethanol production via electrolysis, oxy-fuel combustion, water-gas shift reaction, and LNG cold energy recovery</p>
Gibbs free energy change for the oxygen reduction reaction in solution
<p>Gibbs free energy change for the oxygen reduction reaction in solution on three singe atom catalysts with planar, arched, and vertical configuration.</p>
Acute Effect of Capsimax on Resistance Exercise Performance, Muscle Oxygenation, Nitric Oxide Release, Resting Energy Expenditure and Reaction Time
ClinicalTrials.gov study NCT06612658. IPD Sharing: NO. Countries: 1. Publications: 0.
A Randomized Study to Examine the Ability of a Caffeine-Based Energy Drink to Impact Energy Expenditure, Fat Oxidation, Reaction Time, and Other Perceptual Indicators
ClinicalTrials.gov study NCT05998096. IPD Sharing: NO. Countries: 1. Publications: 0.
Psychrotolerant bacterium Sphingomonas glacialis AAP5 harvests light energy using both proton-pumping xanthorhodopsins and bacteriochlorophyll-based reaction centers
GEO Series GSE196609. Sphingomonas glacialis. 28 samples. Type: Expression profiling by high throughput sequencing.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.